Sema3f semaphorin 3F [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sema3fprovided by RGD
Official Full Name: semaphorin 3Fprovided by RGD
Primary source: RGD:1308514
See related: EnsemblRapid:ENSRNOG00000017704 AllianceGenome:RGD:1308514
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: SemaIV
Summary: Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Predicted to be involved in several processes, including nervous system development; semaphorin-plexin signaling pathway; and ventral trunk neural crest cell migration. Predicted to act upstream of or within negative regulation of axon extension involved in axon guidance and trunk neural crest cell migration. Predicted to be active in glutamatergic synapse and plasma membrane. Orthologous to human SEMA3F (semaphorin 3F). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 82.3), Kidney (RPKM 34.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q32

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (117236269..117265206, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (108357629..108386569, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (116439996..116469915, complement)

Chromosome 8 - NC_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sema3F may contribute to the regulation of retinal ganglion cell function or survival.
Title: Down-regulation of semaphorin 3F in rat retinal ganglion cells in response to optic nerve crush.
These results suggest that plexin A3 is expressed in OPCs and immature oligodendrocytes and is involved in OPC migration.
Title: Plexin A3 is involved in semaphorin 3F-mediated oligodendrocyte precursor cell migration.
These data reveal a novel mechanism by which Sema3F can induce hippocampal neuron growth cone collapse.
Title: Sema3F downregulates p53 expression leading to axonal growth cone collapse in primary hippocampal neurons.
In combination with other inhibitory molecules, semaphorin 3F converts estrogenized myometrium to an inhospitable environment for sympathetic nerves.
Title: Estrogen up-regulation of semaphorin 3F correlates with sympathetic denervation of the rat uterus.
These data are consistent with a model whereby Sema3A and 3F, in combination with other guidance molecules, contributes to the navigation of DA axons to their final synaptic targets.
Title: Expression by midbrain dopamine neurons of Sema3A and 3F receptors is associated with chemorepulsion in vitro but a mild in vivo phenotype.
Sema3F in the pretectum suggested a role for this axon guidance molecules in dopaminergic axon pathfinding
Title: Semaphorins 3A, 3C, and 3F in mesencephalic dopaminergic axon pathfinding.
Thus, Sema3F may act as a chemoattractant for the growth cone of cerebellar granule cells through cGMP signaling pathway.
Title: Semaphorin-3F attracts the growth cone of cerebellar granule cells through cGMP signaling pathway.
These data indicate that vascular EC-derived sema 3s inhibit sympathetic axon growth and may thus be a determinant of vascular sympathetic innervation.
Title: Vascular endothelial-derived semaphorin 3 inhibits sympathetic axon growth.
SEMA3F suppresses lung neoplasm progression in an experimental model
Title: Selective suppression of in vivo tumorigenicity by semaphorin SEMA3F in lung cancer cells.

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General gene information

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Markers

RH133726 (e-PCR)
- UniSTS:217009

D3S4519 (e-PCR)
- UniSTS:474593

D3S4520 (e-PCR)
- UniSTS:474594

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables chemorepellent activity	ISO Inferred from Sequence Orthology more info
enables neuropilin binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in branchiomotor neuron axon guidance	ISO Inferred from Sequence Orthology more info
involved_in facial nerve structural organization	ISO Inferred from Sequence Orthology more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative chemotaxis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in nerve development	ISO Inferred from Sequence Orthology more info
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in neural crest cell migration involved in autonomic nervous system development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of postsynapse organization	ISO Inferred from Sequence Orthology more info
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in semaphorin-plexin signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in sympathetic ganglion development	ISO Inferred from Sequence Orthology more info
involved_in sympathetic neuron projection extension	ISO Inferred from Sequence Orthology more info
involved_in sympathetic neuron projection guidance	ISO Inferred from Sequence Orthology more info
involved_in trigeminal nerve structural organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within trunk neural crest cell migration	ISO Inferred from Sequence Orthology more info
involved_in ventral trunk neural crest cell migration	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: semaphorin-3F

Names: sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F; semaphorin IV

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001413830.1 → NP_001400759.1 semaphorin-3F precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

A6I309, D3ZGX9

Related

ENSRNOP00000024193.5, ENSRNOT00000024193.7

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086026.1 Reference GRCr8

Range

117236269..117265206 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063265627.1 → XP_063121697.1 semaphorin-3F isoform X4

UniProtKB/TrEMBL

A0A0G2K0S6, A6I308

Related

ENSRNOP00000100452.1, ENSRNOT00000144059.1
XM_039081590.2 → XP_038937518.1 semaphorin-3F isoform X2

UniProtKB/TrEMBL

A6I309, D3ZGX9

Conserved Domains (3) summary

cd11254
Location:48 → 548

Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)

smart00423
Location:547 → 584

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:608 → 697

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_039081591.2 → XP_038937519.1 semaphorin-3F isoform X3

Related

ENSRNOP00000071565.3, ENSRNOT00000085915.3

Conserved Domains (3) summary

cd11254
Location:65 → 534

Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)

smart00423
Location:533 → 570

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:594 → 683

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_039081588.1 → XP_038937516.1 semaphorin-3F isoform X1

Conserved Domains (3) summary

cd11254
Location:65 → 565

Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)

smart00423
Location:564 → 601

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:625 → 714

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
XM_039081592.2 → XP_038937520.1 semaphorin-3F isoform X5

Conserved Domains (3) summary

smart00423
Location:384 → 421

PSI; domain found in Plexins, Semaphorins and Integrins

cd05871
Location:445 → 534

Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3

cl15693
Location:21 → 385

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_039081593.2 → XP_038937521.1 semaphorin-3F isoform X6

Conserved Domains (1) summary

cl15693
Location:65 → 496

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins